def set_rowfile_plot_options(parser):
import matplotlib
set_formatter(parser)
if os.name == 'posix' and 1:
matplotlib.use('GTkAgg')
parser.run_methods = ['subcommand']
parser.set_usage('%prog [options] [[-i] ROWFILE]')
parser.set_description('Plot data in ROWFILE')
parser.add_option('--input-path',
'-i',
type='file',
metavar='ROWFILE',
help='Specify path to ROWFILE.')
parser.add_option('--print-keys',
action='store_true',
help='Print keys of the rowfile and exit.')
parser.add_option('--x-keys', help='Specify keys for x-axis.')
parser.add_option(
'--y-keys',
help='Specify keys for y-axis. When not specified then use all keys.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='OUTPUT_PATH',
help='Specify output PATH for saving figure.')
def set_regress_options(parser):
from ..io.script_options import get_microscope_options_group, get_io_options_group
set_formatter(parser)
parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH]]')
parser.set_description(
'Apply local regression methods to INPUT_PATH scalar field.')
parser.add_option('--quiet',
dest='verbose',
action='store_false',
help='Disable output messages.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='PATH',
help='Specify output PATH of 3D images.')
parser.add_option(
"--kernel-width",
dest="kernel_width",
type='float',
help="Specify the width of kernel in minimal voxel size unit.")
parser.add_option(
'--link-function',
choices=['identity'],
default='identity',
help=
"Specify link function to transform data before regression analysis.")
get_regress_options_group(parser, group=parser)
parser.add_option_group(get_io_options_group(parser))
parser.add_option_group(get_microscope_options_group(parser))
def set_run_mirrors_options(parser):
set_formatter(parser)
parser.set_usage('%prog [options]')
parser.set_description('Run scanning mirrors.')
if os.name == 'posix':
parser.run_methods = ['subcommand']
from iocbio.scanner.configuration import camera_area_width, camera_area_height
parser.add_option('--roi-x0', type='int', default=1)
parser.add_option('--roi-x1', type='int', default=camera_area_width)
parser.add_option('--roi-y0', type='int', default=1)
parser.add_option('--roi-y1', type='int', default=camera_area_height)
parser.add_option('--orientation-angle', type='float', default=0)
parser.add_option('--pixel-time-usec', type='float')
parser.add_option('--scan-speed', type='float')
parser.add_option('--image-width', type='int')
parser.add_option('--pixel-size-um', type='float')
parser.add_option('--image-height', type='int', default=2)
parser.add_option('--flyback', type='float')
parser.add_option('--flyback-range', type='string')
parser.add_option_group(get_mirror_parameter_options_group(parser))
parser.add_option_group(get_runner_options_group(parser))
try:
parser.add_option_group(get_nidaqmx_options_group(parser))
except ImportError, msg:
print '%s' % (msg)
def set_sumstacks_options(parser):
import numpy
set_formatter(parser)
parser.set_usage(
'%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]')
parser.set_description(
'Sum the stacks in INPUT_PATH and save the result with specified type and format.'
)
parser.add_option('--input-path',
'-i',
type='file',
metavar='INPUT_PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='OUTPUT_PATH',
help='Specify output PATH of 3D images.')
numpy_types = ['<detect>'] + sorted(
set([t.__name__ for t in numpy.typeDict.values()]))
parser.add_option("--output-type",
dest="output_type",
choices=numpy_types,
default=numpy_types[0],
help="Specify output image stack type.")
parser.add_option('--output-ext',
dest='output_ext',
choices=['tif', 'vtk', 'data'],
default='tif',
help="Specify output format extension.")
parser.add_option_group(get_io_options_group(parser))
def set_clusters_options(parser):
set_formatter(parser)
parser.set_usage('%prog [options] [ -i INPUT_PATH ]')
parser.set_description('Find clusters in INPUT_PATH field.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='INPUT_PATH',
dest='input_path',
help='Specify INPUT_PATH.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='OUTPUT_PATH',
dest='output_path',
help='Specify OUTPUT_PATH.')
parser.add_option(
'--detail-size',
dest='detail_size',
type='float',
help='Specify typical size of a detail to be resolved, in micrometers.'
)
from iocbio.ops.script_options import get_regress_options_group
parser.add_option_group(get_regress_options_group(parser))
from iocbio.ops.script_options import get_fft_options_group
parser.add_option_group(get_fft_options_group(parser))
def set_run_mirrors_options(parser):
set_formatter(parser)
parser.set_usage ('%prog [options]')
parser.set_description('Run scanning mirrors.')
if os.name == 'posix':
parser.run_methods = ['subcommand']
from iocbio.scanner.configuration import camera_area_width, camera_area_height
parser.add_option('--roi-x0', type='int', default=1)
parser.add_option('--roi-x1', type='int', default=camera_area_width)
parser.add_option('--roi-y0', type='int', default=1)
parser.add_option('--roi-y1', type='int', default=camera_area_height)
parser.add_option('--orientation-angle', type='float', default=0)
parser.add_option ('--pixel-time-usec', type='float')
parser.add_option ('--scan-speed', type='float')
parser.add_option('--image-width', type='int')
parser.add_option('--pixel-size-um', type='float')
parser.add_option('--image-height', type='int', default=2)
parser.add_option ('--flyback', type='float')
parser.add_option ('--flyback-range', type='string')
parser.add_option_group (get_mirror_parameter_options_group(parser))
parser.add_option_group (get_runner_options_group(parser))
try:
parser.add_option_group (get_nidaqmx_options_group(parser))
except ImportError, msg:
print '%s' % (msg)
def set_convert_options (parser):
import numpy
set_formatter(parser)
parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]')
parser.set_description('Convert INPUT_PATH to specified type and format.')
parser.add_option ('--input-path','-i',
type = 'file', metavar='INPUT_PATH',
help = 'Specify input PATH of 3D images.'
)
parser.add_option ('--output-path','-o',
type = 'file', metavar='OUTPUT_PATH',
help = 'Specify output PATH of 3D images.'
)
numpy_types = ['<detect>'] + sorted(set([t.__name__ for t in numpy.typeDict.values()]))
parser.add_option("--output-type", dest="output_type",
choices = numpy_types, default = numpy_types[0],
help="Specify output image stack type.")
parser.add_option("--scale",
action="store_true", dest="scale",
help='Specify whether to scale stack to the limits of the output type.')
parser.add_option("--no-scale",
action="store_false", dest="scale",
help='See ``--scale`` option.')
parser.add_option('--normalize',
choices = ['none', 'unit volume'],
help = 'Specify normalization.'
)
parser.add_option('--output-ext', dest='output_ext',
choices = ['tif', 'vtk', 'data'],
default = 'tif',
help="Specify output format extension.")
parser.add_option_group(get_tiff_options_group(parser))
def set_sumstacks_options (parser):
import numpy
set_formatter(parser)
parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]')
parser.set_description('Sum the stacks in INPUT_PATH and save the result with specified type and format.')
parser.add_option ('--input-path','-i',
type = 'file', metavar='INPUT_PATH',
help = 'Specify input PATH of 3D images.'
)
parser.add_option ('--output-path','-o',
type = 'file', metavar='OUTPUT_PATH',
help = 'Specify output PATH of 3D images.'
)
numpy_types = ['<detect>'] + sorted(set([t.__name__ for t in numpy.typeDict.values()]))
parser.add_option("--output-type", dest="output_type",
choices = numpy_types, default = numpy_types[0],
help="Specify output image stack type.")
parser.add_option('--output-ext', dest='output_ext',
choices = ['tif', 'vtk', 'data'],
default = 'tif',
help="Specify output format extension.")
parser.add_option_group(get_io_options_group(parser))
def set_apply_noise_options(parser):
parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH] ]')
set_formatter(parser)
parser.set_description('Apply noise to INPUT_PATH scalar field.')
parser.add_option('--quiet',
dest='verbose',
action='store_false',
default=True,
help='Disable output messages.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='PATH',
help='Specify output PATH of 3D images.')
parser.add_option(
"--noise-type",
dest='noise_type',
choices=['poisson'],
default='poisson',
help='Specify noise type.',
)
def set_deconvolve_with_sphere_options (parser):
set_formatter(parser)
parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ] ]')
parser.set_description('Deconvolve INPUT_PATH with sphere.')
parser.add_option ('--sphere-diameter', dest='diameter',
type = 'float',
default = 170,
help = 'Specify sphere diameter in nanometers.')
parser.add_option ('--input-path', '-i',
type = 'file', metavar='PATH',
help = 'Specify input PATH of 3D images.'
)
parser.add_option ('--output-path','-o',
type = 'file', metavar='PATH',
help = 'Specify output PATH of 3D images.'
)
parser.add_option ('--max-nof-iterations',
type = 'int', default=10,
help = 'Specify maximum number of iterations.')
parser.add_option('--convergence-epsilon',
type = 'float', default=0.05,
help = 'Specify small positive number that determines the window for convergence criteria.')
from ..ops.script_options import get_fft_options_group
from ..io.script_options import get_microscope_options_group
parser.add_option_group(get_fft_options_group (parser))
parser.add_option_group(get_rltv_options_group (parser))
parser.add_option_group(get_microscope_options_group (parser))
def set_ome_options (parser):
import numpy
set_formatter(parser)
parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]')
parser.set_description('Convert INPUT_PATH to OME-TIFF file.')
parser.add_option ('--input-path','-i',
type = 'file', metavar='INPUT_PATH',
help = 'Specify input PATH of 3D images.'
)
def set_deconvolve_options(parser):
set_formatter(parser)
parser.set_usage('%prog [options] [ [-k] PSF_PATH [-i] INPUT_PATH [ [-o] OUTPUT_PATH] ]')
parser.set_description('Deconvolve INPUT_PATH with PSF_PATH.')
add_psflib_options(parser)
parser.add_option('--psf-path','-k', dest = 'psf_path',
type = 'file', metavar='PATH',
help = 'Specify PATH to PSF 3D images.'
)
parser.add_option ('--input-path', '-i',
type = 'file', metavar='PATH',
help = 'Specify input PATH of 3D images.'
)
parser.add_option ('--output-path','-o',
type = 'file', metavar='PATH',
help = 'Specify output PATH of 3D images.'
)
parser.add_option ('--max-nof-iterations',
type = 'int', default=10,
help = 'Specify maximum number of iterations.')
parser.add_option('--convergence-epsilon',
type = 'float', default=0.05,
help = 'Specify small positive number that determines the window for convergence criteria.')
parser.add_option('--degrade-input', action='store_true',
help = 'Degrade input: apply noise to convolved input.')
parser.add_option('--no-degrade-input', action='store_false', dest='degrade_input',
help = 'See ``--degrade-input``.')
parser.add_option('--degrade-input-snr',
type = 'float', default=0.0,
help = 'Specify the signal-to-noise ratio when using --degrade-input.'\
'If set to 0, then snr will be estimated as sqrt(max(input image)).')
parser.add_option ('--first-estimate',
choices = ['input image',
'convolved input image',
'2x convolved input image',
'last result'
],
help = 'Specify first estimate for iteration.')
parser.add_option('--save-intermediate-results',
action = 'store_true',
help = 'Save intermediate results.')
parser.add_option('--no-save-intermediate-results',
dest = 'save_intermediate_results',
action = 'store_false',
help = 'See ``--save-intermediate-results`` option.')
from ..ops.script_options import get_apply_window_options_group
parser.add_option_group(get_apply_window_options_group (parser))
parser.add_option_group(get_rltv_options_group (parser))
from ..ops.script_options import get_fft_options_group
parser.add_option_group(get_fft_options_group (parser))
from ..script_options import get_runner_options_group
parser.add_option_group(get_runner_options_group (parser))
from ..io.script_options import get_io_options_group, get_microscope_options_group
parser.add_option_group(get_microscope_options_group (parser))
def set_ome_options(parser):
import numpy
set_formatter(parser)
parser.set_usage(
'%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]')
parser.set_description('Convert INPUT_PATH to OME-TIFF file.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='INPUT_PATH',
help='Specify input PATH of 3D images.')
def set_strathkelvin929_rate_options(parser):
set_formatter(parser)
parser.set_usage('%prog [options] <channel-files>')
parser.set_description('Re-calculates oxygen respiration rates. Rewrites the channel files unless --tryrun is used.')
parser.add_option('--nof-regression-points', '-n',
type = 'int', default=10,
help = 'Specify the number of regression points. When 0 then use the number from channel files.')
parser.add_option('--tryrun', action = 'store_true',
help = 'Re-calculate rates but do not save rates to file.')
parser.add_option('--no-tryrun', action = 'store_false', dest='tryrun',
help = 'See --tryrun.')
def set_show_options(parser):
set_formatter(parser)
import matplotlib
if os.name == 'posix':
matplotlib.use('GTkAgg')
parser.run_methods = ['subcommand']
parser.set_usage('%prog [options] [ [-i] INPUT_PATH ]')
parser.set_description('Display INPUT_PATH as 3D image.')
parser.add_option ('--input-path', '-i',
type = 'file', metavar='INPUT_PATH',
help = 'Specify input PATH of 3D images.'
)
parser.add_option('--interpolation', default='nearest',
choices = sorted(['bilinear', 'nearest','bicubic', 'spline16',
'spline36', 'hanning', 'hamming', 'hermit',
'kaiser', 'quadric', 'catrom', 'gaussian',
'bessel', 'mitchell', 'sinc', 'lanczos']),
help="Specify image interpolation method.")
#parser.add_option('--roll-axis', choices=['0','1','2'], help='Roll given axis to 0.', default='0')
parser.add_option('--projection', choices=['XY','XZ','YZ'], help='Project image stack to given plane.', default='XY')
parser.add_option('--rgb', action='store_true', default=False,
help="Display as RGB(A) color images.")
parser.add_option('--dpi', type='int', default=96,
help="Specify plot resolution.")
import matplotlib.cm as cm
colormap_names = [name for name in cm.datad if not name.endswith ('_r')]
lcolormap_names = sorted([name for name in colormap_names if name[0].islower()])
ucolormap_names = sorted([name for name in colormap_names if name[0].isupper()])
colormap_names = lcolormap_names + ucolormap_names
parser.add_option('--cmap', choices = colormap_names, default='gray',
help='Specify `colormap <http://matplotlib.sourceforge.net/plot_directive/mpl_examples/pylab_examples/show_colormaps.hires.png>`_.')
parser.add_option ('--invert-cmap', action='store_true', default=False,
help='Invert specified colormap.')
parser.add_option ('--histogram-bins', type='int', default=0,
help = 'Specify the number of bins for histogram. 0 means no histogram.')
parser.add_option ('--auto-scale', action='store_true', default=False,
help = 'Automatically scale each frame.')
parser.add_option ('--view-3d', type='string', default='',
help = 'Specify z=const, y=const, x=const planes for viewing 3d stack.')
parser.add_option ('--output-path', '-o',
type = 'file', metavar='OUTPUT_PATH',
help = 'Specify output PATH for saving figure.'
)
parser.add_option_group(get_io_options_group(parser))
parser.add_option_group(get_microscope_options_group (parser))
def set_estimate_snr_options(parser):
from ..io.script_options import get_microscope_options_group
set_formatter(parser)
parser.set_usage('%prog [options] [ -i INPUT_PATH ]')
parser.set_description(
'Estimate signal to noise ratio from the INPUT_PATH images.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='PATH',
help='Specify input PATH of 3D images.')
parser.add_option_group(get_regress_options_group(parser))
parser.add_option_group(get_microscope_options_group(parser))
def set_clusters_options (parser):
set_formatter(parser)
parser.set_usage ('%prog [options] [ -i INPUT_PATH ]')
parser.set_description('Find clusters in INPUT_PATH field.')
parser.add_option ('--input-path','-i',
type = 'file', metavar='INPUT_PATH', dest='input_path',
help = 'Specify INPUT_PATH.'
)
parser.add_option ('--output-path','-o',
type = 'file', metavar='OUTPUT_PATH', dest='output_path',
help = 'Specify OUTPUT_PATH.'
)
parser.add_option ('--detail-size', dest='detail_size',type = 'float',
help = 'Specify typical size of a detail to be resolved, in micrometers.')
from iocbio.ops.script_options import get_regress_options_group
parser.add_option_group(get_regress_options_group (parser))
from iocbio.ops.script_options import get_fft_options_group
parser.add_option_group(get_fft_options_group (parser))
def set_convert_options(parser):
import numpy
set_formatter(parser)
parser.set_usage(
'%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]')
parser.set_description('Convert INPUT_PATH to specified type and format.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='INPUT_PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='OUTPUT_PATH',
help='Specify output PATH of 3D images.')
numpy_types = ['<detect>'] + sorted(
set([t.__name__ for t in numpy.typeDict.values()]))
parser.add_option("--output-type",
dest="output_type",
choices=numpy_types,
default=numpy_types[0],
help="Specify output image stack type.")
parser.add_option(
"--scale",
action="store_true",
dest="scale",
help='Specify whether to scale stack to the limits of the output type.'
)
parser.add_option("--no-scale",
action="store_false",
dest="scale",
help='See ``--scale`` option.')
parser.add_option('--normalize',
choices=['none', 'unit volume'],
help='Specify normalization.')
parser.add_option('--output-ext',
dest='output_ext',
choices=['tif', 'vtk', 'data'],
default='tif',
help="Specify output format extension.")
parser.add_option_group(get_tiff_options_group(parser))
def set_sarcomere_length_options (parser):
from ..io.script_options import get_microscope_options_group, get_io_options_group
set_formatter (parser)
parser.set_usage('%prog [options] [ -i INPUT_PATH ]')
parser.set_description('Estimate the length of sarcomere.')
parser.add_option ('--input-path','-i',
type = 'file', metavar='PATH',
help = 'Specify input PATH of 3D images.'
)
parser.add_option ('--roi-center-line',
help = 'Specify the coordinates of ROI center line in pixels: x0,y0,x1,y1')
parser.add_option ('--roi-width',
type = 'int',
help = 'Specify the width of ROI in pixels')
parser.add_option ('--nof-points',
type = 'int', default = 512,
help = 'Specify the number of interpolation points.')
parser.add_option_group(get_io_options_group(parser))
parser.add_option_group(get_microscope_options_group(parser))
def set_apply_window_options(parser):
from ..io.script_options import get_microscope_options_group
set_formatter(parser)
parser.set_usage('%prog [options] [ INPUT_PATH [OUTPUT_PATH]]')
parser.set_description('Apply smooth window to INPUT_PATH scalar field.')
parser.add_option('--quiet',
dest='verbose',
action='store_false',
default=True,
help='Disable output messages.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='PATH',
help='Specify output PATH of 3D images.')
get_apply_window_options_group(parser, group=parser)
parser.add_option_group(get_microscope_options_group(parser))
def set_strathkelvin929_rate_options(parser):
set_formatter(parser)
parser.set_usage('%prog [options] <channel-files>')
parser.set_description(
'Re-calculates oxygen respiration rates. Rewrites the channel files unless --tryrun is used.'
)
parser.add_option(
'--nof-regression-points',
'-n',
type='int',
default=10,
help=
'Specify the number of regression points. When 0 then use the number from channel files.'
)
parser.add_option('--tryrun',
action='store_true',
help='Re-calculate rates but do not save rates to file.')
parser.add_option('--no-tryrun',
action='store_false',
dest='tryrun',
help='See --tryrun.')
def set_sarcomere_length_options(parser):
from ..io.script_options import get_microscope_options_group, get_io_options_group
set_formatter(parser)
parser.set_usage('%prog [options] [ -i INPUT_PATH ]')
parser.set_description('Estimate the length of sarcomere.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='PATH',
help='Specify input PATH of 3D images.')
parser.add_option(
'--roi-center-line',
help='Specify the coordinates of ROI center line in pixels: x0,y0,x1,y1'
)
parser.add_option('--roi-width',
type='int',
help='Specify the width of ROI in pixels')
parser.add_option('--nof-points',
type='int',
default=512,
help='Specify the number of interpolation points.')
parser.add_option_group(get_io_options_group(parser))
parser.add_option_group(get_microscope_options_group(parser))
def set_convolve_options(parser):
from ..microscope.script_options import add_psflib_options
set_formatter(parser)
parser.set_usage(
'%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ] ]')
parser.set_description('Convolve INPUT_PATH with KERNEL_PATH.')
add_psflib_options(parser)
parser.add_option('--kernel-path',
'-k',
type='file',
metavar='PATH',
help='Specify PATH to 3D images to be used as a kernel.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='PATH',
help='Specify output PATH of 3D images.')
parser.add_option_group(get_fft_options_group(parser))
def set_deconvolve_with_sphere_options(parser):
set_formatter(parser)
parser.set_usage(
'%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ] ]')
parser.set_description('Deconvolve INPUT_PATH with sphere.')
parser.add_option('--sphere-diameter',
dest='diameter',
type='float',
default=170,
help='Specify sphere diameter in nanometers.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='PATH',
help='Specify output PATH of 3D images.')
parser.add_option('--max-nof-iterations',
type='int',
default=10,
help='Specify maximum number of iterations.')
parser.add_option(
'--convergence-epsilon',
type='float',
default=0.05,
help=
'Specify small positive number that determines the window for convergence criteria.'
)
from ..ops.script_options import get_fft_options_group
from ..io.script_options import get_microscope_options_group
parser.add_option_group(get_fft_options_group(parser))
parser.add_option_group(get_rltv_options_group(parser))
parser.add_option_group(get_microscope_options_group(parser))
def set_rowfile_plot_options (parser):
import matplotlib
set_formatter(parser)
if os.name == 'posix' and 1:
matplotlib.use('GTkAgg')
parser.run_methods = ['subcommand']
parser.set_usage ('%prog [options] [[-i] ROWFILE]')
parser.set_description('Plot data in ROWFILE')
parser.add_option ('--input-path', '-i',
type = 'file', metavar='ROWFILE',
help = 'Specify path to ROWFILE.'
)
parser.add_option('--print-keys', action='store_true',
help = 'Print keys of the rowfile and exit.')
parser.add_option('--x-keys',
help = 'Specify keys for x-axis.')
parser.add_option('--y-keys',
help = 'Specify keys for y-axis. When not specified then use all keys.')
parser.add_option ('--output-path', '-o',
type = 'file', metavar='OUTPUT_PATH',
help = 'Specify output PATH for saving figure.'
)
if os.path.basename(root)=='scripts':
for script in files:
script_name = os.path.splitext(script)[0]
package_name = '.'.join(root[len(os.path.dirname(parent_path))+1:].split(os.sep)[:-1])
try:
exec 'import %s.script_options as script_options' % (package_name)
except ImportError, msg:
print msg
continue
try:
set_options = getattr (script_options, 'set_%s_options' % (script_name))
except AttributeError, msg:
print msg
continue
parser = OptionParser()
set_formatter (parser)
parser.add_option('--no-gui', action='store_false', default=True, help='Run script without opening GUI.')
set_options (parser)
parser.prog = 'fparser.%s' % (script_name)
if parser.description is None:
print 'Warning: %s does not have a description (use parser.set_description in %s.script_options.%s)' % (parser.prog, package_name,set_options.__name__)
parser.description = 'PFI'
descr = parser.get_description()
descr_title = descr.lstrip().split('\n')[0]
help = parser.format_help()
help += '''
See also
========
:mod:`%s`
''' % (package_name)
def set_deconvolve_options(parser):
set_formatter(parser)
parser.set_usage(
'%prog [options] [ [-k] PSF_PATH [-i] INPUT_PATH [ [-o] OUTPUT_PATH] ]'
)
parser.set_description('Deconvolve INPUT_PATH with PSF_PATH.')
add_psflib_options(parser)
parser.add_option('--psf-path',
'-k',
dest='psf_path',
type='file',
metavar='PATH',
help='Specify PATH to PSF 3D images.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='PATH',
help='Specify output PATH of 3D images.')
parser.add_option('--max-nof-iterations',
type='int',
default=10,
help='Specify maximum number of iterations.')
parser.add_option(
'--convergence-epsilon',
type='float',
default=0.05,
help=
'Specify small positive number that determines the window for convergence criteria.'
)
parser.add_option('--degrade-input',
action='store_true',
help='Degrade input: apply noise to convolved input.')
parser.add_option('--no-degrade-input',
action='store_false',
dest='degrade_input',
help='See ``--degrade-input``.')
parser.add_option('--degrade-input-snr',
type = 'float', default=0.0,
help = 'Specify the signal-to-noise ratio when using --degrade-input.'\
'If set to 0, then snr will be estimated as sqrt(max(input image)).')
parser.add_option('--first-estimate',
choices=[
'input image', 'convolved input image',
'2x convolved input image', 'last result'
],
help='Specify first estimate for iteration.')
parser.add_option('--save-intermediate-results',
action='store_true',
help='Save intermediate results.')
parser.add_option('--no-save-intermediate-results',
dest='save_intermediate_results',
action='store_false',
help='See ``--save-intermediate-results`` option.')
from ..ops.script_options import get_apply_window_options_group
parser.add_option_group(get_apply_window_options_group(parser))
parser.add_option_group(get_rltv_options_group(parser))
from ..ops.script_options import get_fft_options_group
parser.add_option_group(get_fft_options_group(parser))
from ..script_options import get_runner_options_group
parser.add_option_group(get_runner_options_group(parser))
from ..io.script_options import get_io_options_group, get_microscope_options_group
parser.add_option_group(get_microscope_options_group(parser))
def set_strathkelvin929_options (parser):
set_formatter(parser)
parser.set_usage('%prog')
parser.set_description('Wrapper of Strathkelvin 929 System software, the GUI program.')
def set_estimate_psf_options(parser):
set_formatter(parser)
parser.set_usage(
'%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ] ]')
parser.set_description(
'''Find PSF estimate from the measurments of microspheres.
Intermediate results are saved to INPUT_PATH/iocbio.estimate_psf/
directory and estimated PSF is saved to OUTPUT_PATH
''')
parser.add_option(
"--measurement-path",
'--input-path',
'-i',
type='file',
metavar='INPUT_PATH',
dest='input_path',
help='''Specify PATH to microsphere measurments.\
To select directory PATH, find a file PATH/{PATHINFO.txt, configuration.txt, SCANINFO.txt} and select it.''',
)
parser.add_option("--psf-path",
'--output-path',
'-o',
'-k',
type='file',
metavar='OUTPUT_PATH',
dest='output_path',
help='''Specify PATH for saving estimated PSF.''')
#parser.add_option('--photon-counter-offset',
# type = 'float',
# help = 'Specify photon counter offset.'
# )
parser.add_option(
'--subtract-background-field',
dest='subtract_background_field',
action='store_true',
help=
'Specify that subtraction of a background field should be carried out.'
)
parser.add_option('--no-subtract-background-field',
dest='subtract_background_field',
action='store_false',
help='See ``--subtract-background-field option``.')
parser.add_option("--cluster-background-level",
dest='cluster_background_level',
type='float',
metavar='FLOAT',
help="""\
Specify maximum background level for defining PSF clusters: smaller
value means larger clusters (a good thing) and higher probability of
overlapping clusters (a bad thing); default will be estimated. """)
parser.add_option(
"--psf-field-size",
dest='psf_field_size',
type='float',
default=7,
metavar='FLOAT',
help='Specify PSF field size in lateral and axial resolution units.')
parser.add_option(
"--show-plots",
dest='show_plots',
action='store_true',
help='Show estimated PSF during computation.',
)
parser.add_option(
"--no-show-plots",
dest='show_plots',
action='store_false',
help='See ``--show-plot option``.',
)
parser.add_option(
"--save-intermediate-results",
dest='save_intermediate_results',
action='store_true',
help='Save intermediate results of computation.',
)
parser.add_option('--no-save-intermediate-results',
dest='save_intermediate_results',
action='store_false',
help='See ``--save-intermediate-results`` option.')
parser.add_option(
'--select-candidates',
help=
'Specify which canditates are selected for computing the PSF estimate.'
)
from ..io.script_options import get_io_options_group, get_microscope_options_group
parser.add_option_group(get_io_options_group(parser))
parser.add_option_group(get_microscope_options_group(parser))
def set_strathkelvin929_options(parser):
set_formatter(parser)
parser.set_usage('%prog')
parser.set_description(
'Wrapper of Strathkelvin 929 System software, the GUI program.')
def set_estimate_psf_options (parser):
set_formatter(parser)
parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ] ]')
parser.set_description('''Find PSF estimate from the measurments of microspheres.
Intermediate results are saved to INPUT_PATH/iocbio.estimate_psf/
directory and estimated PSF is saved to OUTPUT_PATH
''')
parser.add_option ("--measurement-path", '--input-path','-i',
type = 'file', metavar='INPUT_PATH', dest='input_path',
help = '''Specify PATH to microsphere measurments.\
To select directory PATH, find a file PATH/{PATHINFO.txt, configuration.txt, SCANINFO.txt} and select it.''',
)
parser.add_option ("--psf-path", '--output-path','-o','-k',
type = 'file', metavar='OUTPUT_PATH', dest='output_path',
help = '''Specify PATH for saving estimated PSF.'''
)
#parser.add_option('--photon-counter-offset',
# type = 'float',
# help = 'Specify photon counter offset.'
# )
parser.add_option('--subtract-background-field', dest='subtract_background_field',
action = 'store_true',
help='Specify that subtraction of a background field should be carried out.')
parser.add_option('--no-subtract-background-field', dest='subtract_background_field',
action = 'store_false',
help='See ``--subtract-background-field option``.')
parser.add_option ("--cluster-background-level",
dest = 'cluster_background_level',
type = 'float', metavar='FLOAT',
help = """\
Specify maximum background level for defining PSF clusters: smaller
value means larger clusters (a good thing) and higher probability of
overlapping clusters (a bad thing); default will be estimated. """)
parser.add_option ("--psf-field-size",
dest = 'psf_field_size',
type = 'float', default=7, metavar='FLOAT',
help = 'Specify PSF field size in lateral and axial resolution units.'
)
parser.add_option ("--show-plots",
dest = 'show_plots', action = 'store_true',
help = 'Show estimated PSF during computation.',
)
parser.add_option ("--no-show-plots",
dest = 'show_plots', action = 'store_false',
help = 'See ``--show-plot option``.',
)
parser.add_option ("--save-intermediate-results",
dest = 'save_intermediate_results', action = 'store_true',
help = 'Save intermediate results of computation.',
)
parser.add_option ('--no-save-intermediate-results',
dest = 'save_intermediate_results', action = 'store_false',
help = 'See ``--save-intermediate-results`` option.'
)
parser.add_option ('--select-candidates',
help = 'Specify which canditates are selected for computing the PSF estimate.')
from ..io.script_options import get_io_options_group, get_microscope_options_group
parser.add_option_group(get_io_options_group (parser))
parser.add_option_group(get_microscope_options_group (parser))
def set_show_options(parser):
set_formatter(parser)
import matplotlib
if os.name == 'posix':
matplotlib.use('GTkAgg')
parser.run_methods = ['subcommand']
parser.set_usage('%prog [options] [ [-i] INPUT_PATH ]')
parser.set_description('Display INPUT_PATH as 3D image.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='INPUT_PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--interpolation',
default='nearest',
choices=sorted([
'bilinear', 'nearest', 'bicubic', 'spline16',
'spline36', 'hanning', 'hamming', 'hermit', 'kaiser',
'quadric', 'catrom', 'gaussian', 'bessel',
'mitchell', 'sinc', 'lanczos'
]),
help="Specify image interpolation method.")
#parser.add_option('--roll-axis', choices=['0','1','2'], help='Roll given axis to 0.', default='0')
parser.add_option('--projection',
choices=['XY', 'XZ', 'YZ'],
help='Project image stack to given plane.',
default='XY')
parser.add_option('--rgb',
action='store_true',
default=False,
help="Display as RGB(A) color images.")
parser.add_option('--dpi',
type='int',
default=96,
help="Specify plot resolution.")
import matplotlib.cm as cm
colormap_names = [name for name in cm.datad if not name.endswith('_r')]
lcolormap_names = sorted(
[name for name in colormap_names if name[0].islower()])
ucolormap_names = sorted(
[name for name in colormap_names if name[0].isupper()])
colormap_names = lcolormap_names + ucolormap_names
parser.add_option(
'--cmap',
choices=colormap_names,
default='gray',
help=
'Specify `colormap <http://matplotlib.sourceforge.net/plot_directive/mpl_examples/pylab_examples/show_colormaps.hires.png>`_.'
)
parser.add_option('--invert-cmap',
action='store_true',
default=False,
help='Invert specified colormap.')
parser.add_option(
'--histogram-bins',
type='int',
default=0,
help='Specify the number of bins for histogram. 0 means no histogram.')
parser.add_option('--auto-scale',
action='store_true',
default=False,
help='Automatically scale each frame.')
parser.add_option(
'--view-3d',
type='string',
default='',
help='Specify z=const, y=const, x=const planes for viewing 3d stack.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='OUTPUT_PATH',
help='Specify output PATH for saving figure.')
parser.add_option_group(get_io_options_group(parser))
parser.add_option_group(get_microscope_options_group(parser))
